The scripts therein reproducibly produce our citations for our data, annual data reports, presentations, and other outreach documents.
This code is always in development. Find code used for various reports in the code releases.
Emily Markowitz (Emily.Markowitz AT noaa.gov; @EmilyMarkowitz-NOAA)
[Previously] Liz Dawson (Liz.Dawson AT noaa.gov; @liz-dawson-NOAA)
Alaska Fisheries Science Center,
National Marine Fisheries Service,
National Oceanic and Atmospheric Administration,
Seattle, WA 98115
As you, a GAP team member, publishes, that publication should be codified and linked within the
bibliography.bibfile so you and your peers accurately and appropriately cite your work. Learn how to contribute in the Suggestions and Comments section.
A shared citation repository has several benefits for the team:
- We all consistently format and use the most up-to-date citations
- We have an increasingly-complete list of all papers done by us and our colleagues
- The bib file is very versatile and can be pulled directly into any project by URL link
- We can manage our citations as a group instead of individually (e.g., as if we all shared an Endnote, Zotero, or other citation manager)
- We can collectively add and improve citations as new papers, data products, websites, presentatinos, and other resources are published
What citations should be added to the
bibliography.bib
file in this repository?
- journal articles
- tech memos
- stock assessments
- data
- websites
- laws and regulation
- presentations
- … and more! Any resource that anyone in the GAP group may need to cite!
**Find a print out of all of the citations currently included in this repo’s
bibliography.bibin this pdf document.* *
Citation styles provide the particular formats for in-text citations and bibliographies that appear in your research paper. Usually, the choice of citation style will be based on the discipline in which you are writing. Often a journal will indicate the citation style he/she would like you to use.
The NOAA Library now recommends that we use American Psychological Association 7th edition (no ampersand) for citing in NOAA technical memorandums and other NOAA process report publications. Learn more about APA 7th from this Purdue Owl resoure.
The citation style guide for APA 7th can be downloaded from github. This independent open source Citation Style Language (CSL) project aims to facilitate scholarly communication by automating the formatting of citations and bibliographies.
BibTex is a bibliographic tool that is used with LaTeX to help organize the user’s references and create a bibliography. A BibTex user creates a bibliography file that is separate from the LaTeX source file, with a file extension of .bib. Each reference in the bibliography file is formatted with a certain structure and is given a “key” by which the author can refer to it in the source file.
- Aleutian Islands (AI) (Von Szalay et al., 2023)
- Triennial (1990s)/Biennial since 2000 in even years
- Modified Index-Stratified Random of Successful Stations Survey Design
- Eastern Bering Sea Slope (BSS) (Hoff, 2016)
- Intermittent (funding dependent)
- Modified Index-Stratified Random of Successful Stations Survey Design
- Eastern Bering Sea Shelf (EBS) (Markowitz et al., 2024)
- Annual
- Fixed stations at center of 20 x 20 nm grid
- Gulf of Alaska (GOA) (Siple et al., 2024)
- Triennial (1990s)/Biennial since 2001 in odd years
- Stratified Random Survey Design
- Northern Bering Sea (NBS) (Markowitz et al., 2024)
- Biennial/Annual
- Fixed stations at center of 20 x 20 nm grid
Sourcing directly from github requires internet access, but ensures that you will always have the most up to date citation style library and bibliography references.
---
title: "untitled"
date: "`r paste0(format(Sys.time(), '%B %d, %Y'))`"
output: html_document
csl: "https://raw.githubusercontent.com/citation-style-language/styles/master/apa-no-ampersand.csl"
bibliography: "https://raw.githubusercontent.com/afsc-gap-products/citations/main/cite/bibliography.bib"
---To download the CSL and save it to your project, you can use the following code:
csl <- readLines("https://raw.githubusercontent.com/citation-style-language/styles/master/apa-no-ampersand.csl")
readr::write_lines(x = csl, file = "./cite/citestyle.csl")
bib <- readLines("https://raw.githubusercontent.com/afsc-gap-products/citations/main/cite/bibliography.bib")
readr::write_lines(x = bib, file = "./cite/bibliography.csl")Add the link to the
.bib
and
.csl
files in the YAML of your rmarkdown ro quarto file like so:
Note that “../” before the file names refers to directory navigation.
---
title: "untitled"
date: "`r paste0(format(Sys.time(), '%B %d, %Y'))`"
output: html_document
csl: "../cite/citestyle.csl"
bibliography: "../cite/bibliography.bib"
---Zotero
Endnote
Doesn’t work as well as it should. Please submit a pull request or edit
this README if anyone finds a better solution. However, it should work
something like this:
Step 1: Open EndNote and select File > Import > File
File >
Import > File
Step 2: Open EndNote and select the .bib file you wish to import.
.bib file
you wish to import.
Step 3: Select the import filter file you wish to import. For Bibtex, you’ll have to select “Other filters” and then “BibTex”. However, something seems to be wrong with the filter file and… it only kind of works.
Use the [@...] notation in your rmarkdown or quarto call a
reference number for a citation.
For example, here are **Annual Bering Sea Data Report** [@2022NEBS2023; @GOA2018; @AI2022; @RN979]. Which renders as: “For example, here are Annual Bering Sea Data Report (Hoff, 2016; Markowitz et al., 2023; Von Szalay et al., 2023; Von Szalay and Raring, 2018).”
Naturally, without writing anything else, references will appear at the
of the document. If you want them to render at a specific place in your
document, call this code <div id="refs"></div> which renders as:
Hoff, G. R. (2016). Results of the 2016 eastern Bering Sea upper continental slope survey of groundfishes and invertebrate resources (NOAA Tech. Memo. NOAA-AFSC-339). U.S. Dep. Commer. https://doi.org/10.7289/V5/TM-AFSC-339
Markowitz, E. H., Dawson, E. J., Anderson, A. B., Rohan, S. K., Charriere, N. E., Prohaska, B. K., and Stevenson, D. E. (2023). Results of the 2022 eastern and northern Bering Sea continental shelf bottom trawl survey of groundfish and invertebrate fauna (NOAA Tech. Memo. NMFS-AFSC-469; p. 213). U.S. Dep. Commer. https://doi.org/10.25923/rt50-th19
Markowitz, E. H., Dawson, E. J., Wassermann, S., Anderson, A. B., Rohan, S. K., Charriere, B. K., and Stevenson, D. E. (2024). Results of the 2023 eastern and northern Bering Sea continental shelf bottom trawl survey of groundfish and invertebrate fauna (NOAA Tech. Memo. NMFS-AFSC-487; p. 242). U.S. Dep. Commer. https://doi.org/10.25923/2mry-yx09
Siple, M. C., Szalay, P. G. von, Raring, N. W., Dowlin, A. N., and Riggle, B. C. (2024). Data report: 2023 gulf of alaska bottom trawl survey (NOAA Tech. Memo. AFSC processed report; 2024-09). U.S. Dep. Commer. https://doi.org/10.25923/gbb1-x748
Von Szalay, P. G., and Raring, N. W. (2018). Data report: 2017 Gulf of Alaska bottom trawl survey (NOAA Tech. Memo. NMFS-AFSC-374). U.S. Dep. Commer. https://doi.org/10.7289/V5/TM-AFSC-374
Von Szalay, P. G., Raring, N. W., Siple, M. C., Dowlin, A. N., Riggle, B. C., and Laman, E. A. and. (2023). Data report: 2022 Aleutian Islands bottom trawl survey (AFSC Processed Rep. No. 2023-07; p. 230). U.S. Dep. Commer. https://doi.org/10.25923/85cy-g225
This repository is meant to act as a resource for all members of GAP and
beyond. Do you see that a citation is missing from our .bib file,
needs to be edited or you have a new publication? Please add it by
submitting a pull
request or
speaking to one of the repository maintainers.
To learn more about the elements of a bibtext citation, refer to:
Common formatting questions, answered (feel free to add!)
- ‘in review’ or ‘in press’: use
year = {in review}andyear = {in press}, respectively. - Reference numbers must be unique: When entering a new citation,
ensure that the reference number is not used anywhere else in the
.bibdoc. - Finding pre-formatted citations: While not perfect, the below resources can use DOIs or other paper identifiers to find and construct bibliographies in the right format for you:
- Forced case-sensitivity: Use
{...}to force capitalization. This may be needed for proper nouns. For exampletitle = {Results of the 2021 eastern and northern {Bering Sea} continental shelf bottom trawl survey of groundfish and invertebrate fauna}. - Listing DOIs: While the whole link for a DOI may be
https://doi.org/10.25923/9c3r-xp53, only list the text after the
“https://doi.org/” in the
.bibfile as such:doi = {10.25923/9C3R-XP53}. - Use Journal abbreviations: Journal abbreviations can be found
through the Web of
Science
for any given scientific journal as such
journal = {Fish. Oceanogr.}.
To make sure all bibliography listed in the .bib file are consistent,
please refer to these common bibliography types and examples:
NOAA publications are listed and searchable on the NOAA website and AFSC website.
@techreport{RN888,
author = {Alton, M. S. and Bakkala, R. G. and Walters G. E. and Munro, P. T.},
title = {Greenland turbot {(\emph{Reinhardtius hippoglossoides})} of the eastern {Bering Sea} and {Aleutian Islands} region},
url = {https://spo.nmfs.noaa.gov/content/tr-71-greenland-turbot-reinhardtius-hippoglossoides-eastern-bering-sea-and-aleutian-islands},
year = {1998},
publisher = {{U.S. Dep. Commer.}},
type = {NOAA Tech. Rep.},
number = {NMFS-71}
}
@techreport{2021NEBS2022,
author = {Markowitz, E. H. and Dawson, E. J. and Charriere, N. E. and Prohaska, B. K. and Rohan, S. K. and Stevenson, D. E. and Britt, L. L.},
title = {Results of the 2021 eastern and northern {Bering Sea} continental shelf bottom trawl survey of groundfish and invertebrate fauna},
publisher = {{U.S. Dep. Commer.}},
year = {2022},
type = {NOAA Tech. Memo.},
copyright = {Public domain},
number = {NMFS-F/SPO-452},
pages = {227},
doi = {10.25923/g1ny-y360},
url = {https://repository.library.noaa.gov/view/noaa/47710}
}
@techreport{RN920,
author = {Pereyra, W. T. and Reeves, J. E. and Bakkala, R. G.},
title = {Demersal fish and shellfish resources of the eastern {Bering Sea} in the baseline year 1975},
publisher = {U.S. Dep. Commer.},
type = {NOAA Processed Rep.},
year = {1976},
copyright = {Public domain}
}@book{NPFMC2022,
author = {{The Plan Team for the Groundfish Fisheries of the Bering Sea and Aleutian Islands}},
title = {Stock assessment and fishery evaluation report for the groundfish resources of the {Bering Sea/Aleutian Islands} regions},
institution = {North {Pacific} Fishery Management Council},
address = {605 W. 4th Ave., Anchorage, AK 99501},
year = {2022},
url = {https://www.fisheries.noaa.gov/alaska/population-assessments/north-pacific-groundfish-stock-assessments-and-fishery-evaluation}
}
@book{NPFMCBSAIcrab2022,
author = {{The Plan Team for the Groundfish Fisheries of the Bering Sea and Aleutian Islands}},
title = {Stock Assessment and Fishery Evaluation Report for the King and Tanner Crab Fisheries of the {Bering Sea} and {Aleutian Islands} Regions},
institution = {North {Pacific} Fishery Management Council},
address = {605 W. 4th Ave., Anchorage, AK 99501},
year = {2022},
url = {https://meetings.npfmc.org/CommentReview/DownloadFile?p=c0a7a6cc-fed5-4369-a441-b487db9bd60f.pdf&fileName=BSAI%20Crab%20SAFE%202022%20Introduction.pdf}
}
@inbook{SS2022ch6,
author = {Shotwell, S. K. and Bryan, M and Hanselman, D. H. and Markowitz, E. H. and Siddon, E. and Spies, I. and Sullivan, J.},
title = {{NPFMC Bering Sea and Aleutian Islands SAFE}},
chapter = {Chapter 6. Assessment of the arrowtooth flounder stock in the {Bering Sea} and {Aleutian Islands}},
publisher = {North Pacific Fishery Management Council},
address = {605 W. 4th Ave., Anchorage, AK 99501},
year = {2022},
url = {https://apps-afsc.fisheries.noaa.gov/Plan_Team/2022/BSAIatf.pdf}
}@article{RN929,
author = {Spencer, P. D.},
title = {Density‐independent and density‐dependent factors affecting temporal changes in spatial distributions of eastern {Bering Sea} flatfish},
doi = {10.1111/j.1365-2419.2008.00486.x},
journal = {Fish. Oceanogr.},
publisher = {Wiley},
volume = {17},
number = {5},
pages = {396-410},
ISSN = {1054-6006},
year = {2008}
}
@article{Fedewaetal2020,
author = {Fedewa, E.J. and Jackson, T.M. and Richar, J.I. and Gardner, J.L. and Litzow, M.A.},
title = {Recent shifts in northern {Bering Sea} snow crab {(\emph{Chionoecetes opilio})} size structure and the potential role of climate-mediated range contraction},
journal = {Deep Sea Res. Part II Top. Stud. Oceanogr.},
doi = {10.1016/j.dsr2.2020.104878},
url = {https://www.sciencedirect.com/science/article/pii/S0967064520301284},
volume = {104878},
pages = {181–182},
year = {2020}
}@misc{2021NBSCommunity,
title = {2021 northern {Bering Sea} groundfish and crab trawl survey highlights},
author = {Britt, L. L. and Markowitz, E. H. and Dawson, E. J. and Charriere, N. E. and Prohaska, B. K. and Rohan, S. K. and Stevenson, D. E. and Britt, L. L.},
year = {2021},
type = {Outreach},
copyright = {Public domain},
howpublished = {https://youtu.be/putpYJtPRF8}
}
@misc{2022NEBS2022PlanTeamPres,
author = {Stevenson, D. E. and Markowitz, E. H. and Dawson, E. J. and Charriere, N. E. and Prohaska, B. K. and Rohan, S. K. and Britt, L. L.},
title = {Results of the 2022 eastern and northern {Bering Sea} continental shelf bottom trawl survey of groundfish and invertebrate fauna},
year = {2022},
publisher = {North Pacific Fishery Management Council},
copyright = {Public domain},
howpublished = {https://meetings.npfmc.org/CommentReview/DownloadFile?p=02e397c4-a1cc-46eb-b2ae-1c3cc368e682.pdf&fileName=2022_EBSsurvey_planteam.pdf}
}@misc{FOSSAFSCData,
author = {{NOAA Fisheries Alaska Fisheries Science Center}},
year = {2023},
title = {Fisheries One Stop Shop Public Data: RACE Division Bottom Trawl Survey Data Query},
howpublished = {https://www.fisheries.noaa.gov/foss/f?p=215:28:2283554735243:::::},
publisher = {{U.S. Dep. Commer.}},
copyright = {Public Domain}
}
@misc{DisMAPDataPortal,
author = {{NOAA Fisheries}},
year = {2023},
title = {Distribution Mapping and Analysis Portal (DisMAP) data records},
howpublished = {https://apps-st.fisheries.noaa.gov/dismap/},
publisher = {{U.S. Dep. Commer.}},
copyright = {Public Domain}
}From suggested citations
The {trawllight} created by @sean-rohan-NOAA has a built in citation that can be cited like below.
To find the citation:
require(remotes)
remotes::install_github("afsc-gap-products/trawllight")To use the citation:
library(trawllight)
utils::citation("trawllight")FALSE To cite package 'trawllight' in publications use:
FALSE
FALSE Rohan S, Laman N (2024). _trawllight: Derive apparent optical properties from trawl-mounted light sensors_. R package version 3.2.0, commit
FALSE 240ac9594c6817266159271cc63bf57dec219fa4, <https://github.com/afsc-gap-products/trawllight>.
FALSE
FALSE A BibTeX entry for LaTeX users is
FALSE
FALSE @Manual{,
FALSE title = {trawllight: Derive apparent optical properties from trawl-mounted light
FALSE sensors},
FALSE author = {Sean Rohan and Ned Laman},
FALSE year = {2024},
FALSE note = {R package version 3.2.0, commit 240ac9594c6817266159271cc63bf57dec219fa4},
FALSE url = {https://github.com/afsc-gap-products/trawllight},
FALSE }
From Zenodo
For packages not on CRAN, package builders can use Zenodo to cite their R packages.
The {trawllight} created by @sean-rohan-NOAA has a citation on zenodo that can be cited like below.
@software{sean_rohan_2020_3700877,
author = {sean-rohan},
title = {sean-rohan/trawllight: Light conversion features},
month = mar,
year = 2020,
publisher = {Zenodo},
version = {1.2.0},
doi = {10.5281/zenodo.3700877},
url = {https://doi.org/10.5281/zenodo.3700877}
}Example coming soon! (e.g., Magnuson-Stevenson)
Example coming soon! (e.g., NOAA Fisheries’ website)
@book{RN912,
author = {Mecklenburg, C. W. and Mecklenburg, T. A. and Thorsteinson, L. K.},
title = {Fishes of {Alaska}},
ISBN = {1888569077},
year = {2002}
}Here is how the user can find all of the packages ever installed on the local computer
PKG <- tibble::tibble(
Package = names(installed.packages()[,3]),
Version = unname(installed.packages()[,3])
)
head(PKG)FALSE # A tibble: 6 × 2
FALSE Package Version
FALSE <chr> <chr>
FALSE 1 abind 1.4-8
FALSE 2 akfingapdata 0.1.0
FALSE 3 akgfmaps 3.5.3
FALSE 4 antiword 1.3.4
FALSE 5 askpass 1.2.1
FALSE 6 assertthat 0.2.1
Here is how the user can find all of the packages ever installed on the local computer
PKG <- names(sessionInfo()[7][[1]])
PKGFALSE NULL
Then to cite the packages loaded for this R project, create a .bib file for R packages:
knitr::write_bib(x = PKG,
file = "./cite/bibliography_RPack.bib")Which looks like
FALSE [1] "@Manual{R-ggplot2,"
FALSE [2] " title = {ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics},"
FALSE [3] " author = {Hadley Wickham and Winston Chang and Lionel Henry and Thomas Lin Pedersen and Kohske Takahashi and Claus Wilke and Kara Woo and Hiroaki Yutani and Dewey Dunnington},"
FALSE [4] " year = {2023},"
FALSE [5] " note = {R package version 3.4.1},"
FALSE [6] " url = {https://CRAN.R-project.org/package=ggplot2},"
FALSE [7] "}"
FALSE [8] ""
And add your new bibliography file to your YAML:
---
title: "untitled"
date: "`r paste0(format(Sys.time(), '%B %d, %Y'))`"
output: html_document
csl: "https://raw.githubusercontent.com/citation-style-language/styles/master/apa-no-ampersand.csl"
bibliography: "../cite/bibliography_RPack.bib"
---Other resources for developing bibliographies for papers and reports include:
- The
{journals}package in nmfs-fish-tools - The
{RefManageR}package for searching .bib files
If you see that the data, product, or metadata can be improved, you are invited to create a pull request, submit an issue to the GitHub organization, or submit an issue to the code’s repository.
sessionInfo()FALSE R version 4.4.1 (2024-06-14 ucrt)
FALSE Platform: x86_64-w64-mingw32/x64
FALSE Running under: Windows 10 x64 (build 19045)
FALSE
FALSE Matrix products: default
FALSE
FALSE
FALSE locale:
FALSE [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
FALSE [5] LC_TIME=English_United States.utf8
FALSE
FALSE time zone: America/Los_Angeles
FALSE tzcode source: internal
FALSE
FALSE attached base packages:
FALSE [1] stats graphics grDevices utils datasets methods base
FALSE
FALSE other attached packages:
FALSE [1] trawllight_3.2.0 ggplot2_3.5.1 janitor_2.2.0 readr_2.1.5 here_1.0.1 magrittr_2.0.3 dplyr_1.1.4 tidyr_1.3.1
FALSE
FALSE loaded via a namespace (and not attached):
FALSE [1] gtable_0.3.6 compiler_4.4.1 tidyselect_1.2.1 stringr_1.5.1 snakecase_0.11.1 scales_1.3.0 yaml_2.3.10 fastmap_1.2.0
FALSE [9] R6_2.5.1 generics_0.1.3 knitr_1.48 readtext_0.91 tibble_3.2.1 munsell_0.5.1 rprojroot_2.0.4 lubridate_1.9.3
FALSE [17] pillar_1.9.0 tzdb_0.4.0 rlang_1.1.4 utf8_1.2.4 stringi_1.8.4 xfun_0.47 timechange_0.3.0 cli_3.6.3
FALSE [25] withr_3.0.2 grid_4.4.1 digest_0.6.37 rstudioapi_0.17.1 hms_1.1.3 lifecycle_1.0.4 vctrs_0.6.5 evaluate_1.0.1
FALSE [33] glue_1.7.0 data.table_1.16.2 colorspace_2.1-1 fansi_1.0.6 rmarkdown_2.28 purrr_1.0.2 httr_1.4.7 tools_4.4.1
FALSE [41] pkgconfig_2.0.3 htmltools_0.5.8.1
This repository is a scientific product and is not official communication of the National Oceanic and Atmospheric Administration, or the United States Department of Commerce. All NOAA GitHub project code is provided on an ‘as is’ basis and the user assumes responsibility for its use. Any claims against the Department of Commerce or Department of Commerce bureaus stemming from the use of this GitHub project will be governed by all applicable Federal law. Any reference to specific commercial products, processes, or services by service mark, trademark, manufacturer, or otherwise, does not constitute or imply their endorsement, recommendation or favoring by the Department of Commerce. The Department of Commerce seal and logo, or the seal and logo of a DOC bureau, shall not be used in any manner to imply endorsement of any commercial product or activity by DOC or the United States Government.
Software code created by U.S. Government employees is not subject to copyright in the United States (17 U.S.C. §105). The United States/Department of Commerce reserve all rights to seek and obtain copyright protection in countries other than the United States for Software authored in its entirety by the Department of Commerce. To this end, the Department of Commerce hereby grants to Recipient a royalty-free, nonexclusive license to use, copy, and create derivative works of the Software outside of the United States.
U.S. Department of Commerce | National Oceanographic and Atmospheric Administration | NOAA Fisheries